#Hide warnings on the notebook
import warnings
warnings.filterwarnings('ignore')
from TaxaFuncExplore.taxaFuncAnalyzer import TaxaFuncAnalyzer
from TaxaFuncExplore.taxaFuncPloter.basic_plot import BasicPlot
from TaxaFuncExplore.taxaFuncPloter.heatmap_plot import HeatmapPlot
from TaxaFuncExplore.taxaFuncPloter.volcano_plot import VolcanoPlot
from TaxaFuncExplore.taxaFuncPloter.tukey_plot import TukeyPlot
from TaxaFuncExplore.taxaFuncPloter.line_plot import LinePlot
from TaxaFuncExplore.taxaFuncPloter.sankey_plot import SankeyPlot
meta_path = 'tests/Sweetener_Meta.txt'
df_path = 'tests/sw.tsv'
sw = TaxaFuncAnalyzer(df_path, meta_path)
display(sw.original_df.head(5))
display(sw.meta_df.head(5))
| Sequence | Proteins | V1_01 | V1_02 | V1_03 | V1_04 | V1_05 | V1_06 | V1_07 | V1_08 | ... | Preferred_name | Preferred_name_prop | GOs | GOs_prop | KEGG_ko | KEGG_ko_prop | KEGG_Pathway | KEGG_Pathway_prop | PFAMs | PFAMs_prop | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | (AccQTag)DGPMPQTNEHVLLAR | MGYG000004756_01173 | 0 | 0 | 0 | 315416 | 0 | 0 | 0 | 143071 | ... | tuf | 1.0 | unknown | 1.0 | ko:K02358 | 1.0 | unknown | 1.0 | GTP_EFTU,GTP_EFTU_D2,GTP_EFTU_D3 | 1.0 |
| 1 | (AccQTag)QPVENAVVLGVVAELAK | MGYG000002517_02511 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | unknown | 1.0 | unknown | 1.0 | ko:K03406 | 1.0 | ko02020,ko02030,map02020,map02030 | 1.0 | 4HB_MCP_1,MCPsignal,dCache_1 | 1.0 |
| 2 | (Acetyl)AAVDATAVSPEELQAK | MGYG000003683_00301;MGYG000001490_01143 | 422996 | 780124 | 1091422 | 984615 | 593835 | 1093220 | 600823 | 861960 | ... | pflB | 1.0 | unknown | 1.0 | ko:K00656 | 1.0 | ko00620,ko00640,ko00650,ko01100,ko01120,map006... | 1.0 | Bac_luciferase,Fer4_12,Gly_radical,PFL-like,Ra... | 1.0 |
| 3 | (Acetyl)ADADIASDDAIKK | MGYG000000212_00409 | 0 | 867943 | 0 | 0 | 0 | 0 | 0 | 0 | ... | unknown | 1.0 | unknown | 1.0 | unknown | 1.0 | unknown | 1.0 | Peripla_BP_4 | 1.0 |
| 4 | (Acetyl)ADQLTEEQIAEFK | sp|P0DP24|CALM2_HUMAN;sp|P0DP25|CALM3_HUMAN;sp... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | unknown | 1.0 | unknown | 1.0 | unknown | 1.0 | unknown | 1.0 | unknown | 1.0 |
5 rows × 213 columns
| Sample | Person | Treatment | Sweetener | Sweetener_detail | |
|---|---|---|---|---|---|
| 0 | V1_01 | V1 | PBS | PBS | PBSB |
| 1 | V1_02 | V1 | Treatment | ISO | ISO |
| 2 | V1_03 | V1 | Treatment | SOR | SORC |
| 3 | V1_04 | V1 | Treatment | ERY | ERY |
| 4 | V1_05 | V1 | Treatment | HSH | HSH |
sw.set_func('Description')
sw.set_multi_tables(level='s')
sw.set_group('Sweetener')
Function number: 4276
Taxa number: 1194
Taxa-Function number: 20739
group is set to Sweetener
{'XYL', 'NDC', 'ADV', 'STE', 'SAC05', 'BAS', 'MAN', 'NEO006', 'REB', 'SOR', 'CYC', 'HSH', 'SAC2', 'ERY', 'NEO2', 'SAA', 'PBS', 'KES', 'ISO', 'ACE005', 'MFE', 'LAC', 'THA2', 'SUC', 'MAL', 'ACE2', 'FOS', 'GLU', 'ASP', 'THA03'}
If an error is entered, the program will give a prompt.
sw.set_func('abc')
--------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In[52], line 1 ----> 1 sw.set_func('abc') File c:\Users\Qing\OneDrive - University of Ottawa\code\TaxaFunc\TaxaFuncExplore\TaxaFuncExplore\taxaFuncAnalyzer.py:43, in TaxaFuncAnalyzer.set_func(self, func) 40 check_list = ['Description', 'eggNOG_OGs', 'COG_category', 41 'Preferred_name', 'GOs', 'KEGG_ko', 'KEGG_Pathway', 'PFAMs'] 42 if func not in check_list: ---> 43 raise ValueError(f'func must be in {check_list}') 44 else: 45 self.func = func ValueError: func must be in ['Description', 'eggNOG_OGs', 'COG_category', 'Preferred_name', 'GOs', 'KEGG_ko', 'KEGG_Pathway', 'PFAMs']
sw.get_stats_peptide_num_in_taxa()
| LCA_level | count | freq | label | |
|---|---|---|---|---|
| 0 | unknown | 3559 | 1.98 | unknown (1.98%) |
| 1 | l | 9110 | 5.06 | l (5.06%) |
| 2 | d | 25437 | 14.12 | d (14.12%) |
| 3 | p | 1202 | 0.67 | p (0.67%) |
| 4 | c | 5532 | 3.07 | c (3.07%) |
| 5 | o | 7907 | 4.39 | o (4.39%) |
| 6 | f | 23773 | 13.20 | f (13.2%) |
| 7 | g | 36299 | 20.15 | g (20.15%) |
| 8 | s | 67295 | 37.36 | s (37.36%) |
bp = BasicPlot(sw)
bp.plot_taxa_stats()
sw.get_stats_taxa_level()
| taxa_level | count | |
|---|---|---|
| 0 | d | 2 |
| 1 | p | 21 |
| 2 | c | 26 |
| 3 | o | 70 |
| 4 | f | 159 |
| 5 | g | 630 |
| 6 | s | 1194 |
bp.plot_taxa_number()
sw.get_stats_func_prop()
| prop | n | freq | label | |
|---|---|---|---|---|
| 0 | 0-0.1 | 1452 | 0.81 | 0-0.1 (0.81%) |
| 1 | 0-0.2 | 5798 | 3.22 | 0-0.2 (3.22%) |
| 2 | 0-0.3 | 5383 | 2.99 | 0-0.3 (2.99%) |
| 3 | 0-0.4 | 4416 | 2.45 | 0-0.4 (2.45%) |
| 4 | 0-0.5 | 3194 | 1.77 | 0-0.5 (1.77%) |
| 5 | 0.5-0.6 | 9272 | 5.15 | 0.5-0.6 (5.15%) |
| 6 | 0.6-0.7 | 6592 | 3.66 | 0.6-0.7 (3.66%) |
| 7 | 0.7-0.8 | 4191 | 2.33 | 0.7-0.8 (2.33%) |
| 8 | 0.8-0.9 | 4607 | 2.56 | 0.8-0.9 (2.56%) |
| 9 | 0.9-1 | 2932 | 1.63 | 0.9-1 (1.63%) |
| 10 | 1 | 132277 | 73.44 | 1 (73.44%) |
bp.plot_prop_stats()
show_label: Whether to show text labels for each pointbp.plot_pca_sns(sw.func_df, 'Description', show_label=False)
<Axes: title={'center': 'PCA of Description (total variance explained: 55.61%)'}, xlabel='PC1 (40.56%)', ylabel='PC2 (15.05%)'>
df_anova = sw.get_stats_anova()
display(df_anova.sort_values(by='P-value'))
| P-value | f-statistic | V1_14 | V2_14 | V3_14 | V4_14 | V5_14 | V1_34 | V2_34 | V3_34 | ... | V1_19 | V2_19 | V3_19 | V4_19 | V5_19 | V1_29 | V2_29 | V3_29 | V4_29 | V5_29 | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Taxon | Description | |||||||||||||||||||||
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eubacterium_I|s__Eubacterium_I ramulus_A | Putative cyclase | 1.069379e-59 | 41.000241 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A | Alpha amylase catalytic | 2.874864e-40 | 20.587759 | 2261304 | 2201322 | 4819914 | 4308406 | 4099658 | 2653869 | 4015319 | 5378878 | ... | 4645589 | 3355361 | 6394572 | 3471225 | 3120889 | 2936049 | 2935611 | 6664403 | 6525077 | 5417808 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Oscillospirales|f__Ruminococcaceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii_G | Synthesizes alpha-1,4-glucan chains using ADP-glucose | 7.839772e-40 | 20.247267 | 2161583 | 1171388 | 1452533 | 547840 | 1226974 | 1436976 | 1340803 | 1374738 | ... | 2287953 | 907358 | 1039238 | 505004 | 564216 | 1998224 | 481404 | 1342607 | 643314 | 941314 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Oscillospirales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii | Putative cyclase | 7.169301e-36 | 17.336740 | 0 | 0 | 0 | 574450 | 245255 | 240240 | 0 | 131981 | ... | 0 | 0 | 0 | 0 | 0 | 475270 | 358287 | 366993 | 829588 | 1802211 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A sp003477525 | Alpha amylase catalytic | 1.162862e-35 | 17.191300 | 752058 | 501677 | 338422 | 406385 | 0 | 257363 | 573499 | 560082 | ... | 637378 | 454122 | 600596 | 200481 | 0 | 305700 | 1161917 | 220976 | 760564 | 255284 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| d__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__UBA7173|s__UBA7173 sp900548705 | Restriction endonuclease EcoRII, N-terminal | 1.000000e+00 | 0.055804 | 9622497 | 0 | 0 | 0 | 0 | 9372924 | 0 | 0 | ... | 6855554 | 0 | 0 | 0 | 0 | 9056019 | 0 | 0 | 0 | 0 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Oscillospirales|f__Ruminococcaceae|g__Gemmiger|s__Gemmiger sp900540775 | Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors | 1.000000e+00 | 0.052012 | 795406 | 0 | 0 | 0 | 0 | 849258 | 0 | 0 | ... | 736983 | 0 | 0 | 0 | 0 | 1166248 | 0 | 0 | 0 | 0 |
| d__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes_A|s__Alistipes_A sp900546005 | Dihydrolipoyl dehydrogenase | 1.000000e+00 | 0.048783 | 821596 | 0 | 0 | 0 | 0 | 756031 | 0 | 0 | ... | 694901 | 0 | 0 | 0 | 0 | 628216 | 0 | 0 | 0 | 198233 |
| d__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sp002493165 | TonB-linked outer membrane protein, SusC RagA family | 1.000000e+00 | 0.045900 | 165038 | 27105959 | 935682 | 1009706 | 2765160 | 1128890 | 17026504 | 960438 | ... | 620187 | 19409901 | 533998 | 1960642 | 1609337 | 0 | 26000938 | 358024 | 361038 | 1921853 |
| d__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei | nuclear chromosome segregation | 1.000000e+00 | 0.021218 | 1295530 | 2616270 | 44453652 | 2191325 | 0 | 2186680 | 3029660 | 29475129 | ... | 2859969 | 3078600 | 43086120 | 666617 | 367647 | 2068236 | 1483282 | 36460724 | 5979153 | 1458923 |
20739 rows × 192 columns
Top 200, f-statistical, fig size: 30*30
hp = HeatmapPlot(sw)
hp.plot_top_taxa_func_heatmap_of_test_res(df_anova, sw.func, 200, 'f', (30,30))
Table size: 20739 x 192 Recommended figure size: width: 40, length: 40, front_title: 20, font_size: 10
<seaborn.matrix.ClusterGrid at 0x18781a360d0>
Top 100, p-value, auto figsize
hp.plot_top_taxa_func_heatmap_of_test_res(df_anova, sw.func, 100, 'p')
Table size: 20739 x 192 Recommended figure size: width: 40, length: 40, front_title: 20, font_size: 10
<seaborn.matrix.ClusterGrid at 0x187818ecdc0>
taxon = 'd__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A'
function = 'Alpha amylase catalytic'
df_tukey = sw.get_stats_tukey_test(taxon_name=taxon, func_name=function)
Multiple Comparison of Means - Tukey HSD, FWER=0.05 ======================================================================== group1 group2 meandiff p-adj lower upper reject ------------------------------------------------------------------------ ACE005 ACE2 102736.2 1.0 -9580060.2742 9785532.6742 False ACE005 ADV 497062.0 1.0 -9185734.4742 10179858.4742 False ACE005 ASP 1149026.0 1.0 -8533770.4742 10831822.4742 False ACE005 BAS -292064.5333 1.0 -8198034.7483 7613905.6816 False ACE005 CYC 601164.2 1.0 -9081632.2742 10283960.6742 False ACE005 ERY 1392532.2 1.0 -8290264.2742 11075328.6742 False ACE005 FOS 1317520.4 1.0 -8365276.0742 11000316.8742 False ACE005 GLU 1976288.8 1.0 -7706507.6742 11659085.2742 False ACE005 HSH 10672654.0 0.0134 989857.5258 20355450.4742 True ACE005 ISO 28356890.8 0.0 18674094.3258 38039687.2742 True ACE005 KES 934088.2 1.0 -8748708.2742 10616884.6742 False ACE005 LAC 399020.4 1.0 -9283776.0742 10081816.8742 False ACE005 MAL 34525732.0 0.0 24842935.5258 44208528.4742 True ACE005 MAN 453252.2 1.0 -7452718.015 8359222.415 False ACE005 MFE -753228.2 1.0 -10436024.6742 8929568.2742 False ACE005 NDC 58992.8 1.0 -9623803.6742 9741789.2742 False ACE005 NEO006 143415.6 1.0 -9539380.8742 9826212.0742 False ACE005 NEO2 333360.4 1.0 -9349436.0742 10016156.8742 False ACE005 PBS 331933.6667 1.0 -7574036.5483 8237903.8816 False ACE005 REB 18206.0 1.0 -9664590.4742 9701002.4742 False ACE005 SAA 1431723.2 1.0 -8251073.2742 11114519.6742 False ACE005 SAC05 -151109.6 1.0 -9833906.0742 9531686.8742 False ACE005 SAC2 82987.6 1.0 -9599808.8742 9765784.0742 False ACE005 SOR 743623.9333 1.0 -7162346.2816 8649594.1483 False ACE005 STE -587363.6 1.0 -10270160.0742 9095432.8742 False ACE005 SUC 594158.2 1.0 -9088638.2742 10276954.6742 False ACE005 THA03 555801.4 1.0 -9126995.0742 10238597.8742 False ACE005 THA2 659406.4 1.0 -9023390.0742 10342202.8742 False ACE005 XYL 1357668.8 1.0 -8325127.6742 11040465.2742 False ACE2 ADV 394325.8 1.0 -9288470.6742 10077122.2742 False ACE2 ASP 1046289.8 1.0 -8636506.6742 10729086.2742 False ACE2 BAS -394800.7333 1.0 -8300770.9483 7511169.4816 False ACE2 CYC 498428.0 1.0 -9184368.4742 10181224.4742 False ACE2 ERY 1289796.0 1.0 -8393000.4742 10972592.4742 False ACE2 FOS 1214784.2 1.0 -8468012.2742 10897580.6742 False ACE2 GLU 1873552.6 1.0 -7809243.8742 11556349.0742 False ACE2 HSH 10569917.8 0.0154 887121.3258 20252714.2742 True ACE2 ISO 28254154.6 0.0 18571358.1258 37936951.0742 True ACE2 KES 831352.0 1.0 -8851444.4742 10514148.4742 False ACE2 LAC 296284.2 1.0 -9386512.2742 9979080.6742 False ACE2 MAL 34422995.8 0.0 24740199.3258 44105792.2742 True ACE2 MAN 350516.0 1.0 -7555454.215 8256486.215 False ACE2 MFE -855964.4 1.0 -10538760.8742 8826832.0742 False ACE2 NDC -43743.4 1.0 -9726539.8742 9639053.0742 False ACE2 NEO006 40679.4 1.0 -9642117.0742 9723475.8742 False ACE2 NEO2 230624.2 1.0 -9452172.2742 9913420.6742 False ACE2 PBS 229197.4667 1.0 -7676772.7483 8135167.6816 False ACE2 REB -84530.2 1.0 -9767326.6742 9598266.2742 False ACE2 SAA 1328987.0 1.0 -8353809.4742 11011783.4742 False ACE2 SAC05 -253845.8 1.0 -9936642.2742 9428950.6742 False ACE2 SAC2 -19748.6 1.0 -9702545.0742 9663047.8742 False ACE2 SOR 640887.7333 1.0 -7265082.4816 8546857.9483 False ACE2 STE -690099.8 1.0 -10372896.2742 8992696.6742 False ACE2 SUC 491422.0 1.0 -9191374.4742 10174218.4742 False ACE2 THA03 453065.2 1.0 -9229731.2742 10135861.6742 False ACE2 THA2 556670.2 1.0 -9126126.2742 10239466.6742 False ACE2 XYL 1254932.6 1.0 -8427863.8742 10937729.0742 False ADV ASP 651964.0 1.0 -9030832.4742 10334760.4742 False ADV BAS -789126.5333 1.0 -8695096.7483 7116843.6816 False ADV CYC 104102.2 1.0 -9578694.2742 9786898.6742 False ADV ERY 895470.2 1.0 -8787326.2742 10578266.6742 False ADV FOS 820458.4 1.0 -8862338.0742 10503254.8742 False ADV GLU 1479226.8 1.0 -8203569.6742 11162023.2742 False ADV HSH 10175592.0 0.0265 492795.5258 19858388.4742 True ADV ISO 27859828.8 0.0 18177032.3258 37542625.2742 True ADV KES 437026.2 1.0 -9245770.2742 10119822.6742 False ADV LAC -98041.6 1.0 -9780838.0742 9584754.8742 False ADV MAL 34028670.0 0.0 24345873.5258 43711466.4742 True ADV MAN -43809.8 1.0 -7949780.015 7862160.415 False ADV MFE -1250290.2 1.0 -10933086.6742 8432506.2742 False ADV NDC -438069.2 1.0 -10120865.6742 9244727.2742 False ADV NEO006 -353646.4 1.0 -10036442.8742 9329150.0742 False ADV NEO2 -163701.6 1.0 -9846498.0742 9519094.8742 False ADV PBS -165128.3333 1.0 -8071098.5483 7740841.8816 False ADV REB -478856.0 1.0 -10161652.4742 9203940.4742 False ADV SAA 934661.2 1.0 -8748135.2742 10617457.6742 False ADV SAC05 -648171.6 1.0 -10330968.0742 9034624.8742 False ADV SAC2 -414074.4 1.0 -10096870.8742 9268722.0742 False ADV SOR 246561.9333 1.0 -7659408.2816 8152532.1483 False ADV STE -1084425.6 1.0 -10767222.0742 8598370.8742 False ADV SUC 97096.2 1.0 -9585700.2742 9779892.6742 False ADV THA03 58739.4 1.0 -9624057.0742 9741535.8742 False ADV THA2 162344.4 1.0 -9520452.0742 9845140.8742 False ADV XYL 860606.8 1.0 -8822189.6742 10543403.2742 False ASP BAS -1441090.5333 1.0 -9347060.7483 6464879.6816 False ASP CYC -547861.8 1.0 -10230658.2742 9134934.6742 False ASP ERY 243506.2 1.0 -9439290.2742 9926302.6742 False ASP FOS 168494.4 1.0 -9514302.0742 9851290.8742 False ASP GLU 827262.8 1.0 -8855533.6742 10510059.2742 False ASP HSH 9523628.0 0.0607 -159168.4742 19206424.4742 False ASP ISO 27207864.8 0.0 17525068.3258 36890661.2742 True ASP KES -214937.8 1.0 -9897734.2742 9467858.6742 False ASP LAC -750005.6 1.0 -10432802.0742 8932790.8742 False ASP MAL 33376706.0 0.0 23693909.5258 43059502.4742 True ASP MAN -695773.8 1.0 -8601744.015 7210196.415 False ASP MFE -1902254.2 1.0 -11585050.6742 7780542.2742 False ASP NDC -1090033.2 1.0 -10772829.6742 8592763.2742 False ASP NEO006 -1005610.4 1.0 -10688406.8742 8677186.0742 False ASP NEO2 -815665.6 1.0 -10498462.0742 8867130.8742 False ASP PBS -817092.3333 1.0 -8723062.5483 7088877.8816 False ASP REB -1130820.0 1.0 -10813616.4742 8551976.4742 False ASP SAA 282697.2 1.0 -9400099.2742 9965493.6742 False ASP SAC05 -1300135.6 1.0 -10982932.0742 8382660.8742 False ASP SAC2 -1066038.4 1.0 -10748834.8742 8616758.0742 False ASP SOR -405402.0667 1.0 -8311372.2816 7500568.1483 False ASP STE -1736389.6 1.0 -11419186.0742 7946406.8742 False ASP SUC -554867.8 1.0 -10237664.2742 9127928.6742 False ASP THA03 -593224.6 1.0 -10276021.0742 9089571.8742 False ASP THA2 -489619.6 1.0 -10172416.0742 9193176.8742 False ASP XYL 208642.8 1.0 -9474153.6742 9891439.2742 False BAS CYC 893228.7333 1.0 -7012741.4816 8799198.9483 False BAS ERY 1684596.7333 1.0 -6221373.4816 9590566.9483 False BAS FOS 1609584.9333 1.0 -6296385.2816 9515555.1483 False BAS GLU 2268353.3333 1.0 -5637616.8816 10174323.5483 False BAS HSH 10964718.5333 0.0002 3058748.3184 18870688.7483 True BAS ISO 28648955.3333 0.0 20742985.1184 36554925.5483 True BAS KES 1226152.7333 1.0 -6679817.4816 9132122.9483 False BAS LAC 691084.9333 1.0 -7214885.2816 8597055.1483 False BAS MAL 34817796.5333 0.0 26911826.3184 42723766.7483 True BAS MAN 745316.7333 1.0 -4845048.4175 6335681.8842 False BAS MFE -461163.6667 1.0 -8367133.8816 7444806.5483 False BAS NDC 351057.3333 1.0 -7554912.8816 8257027.5483 False BAS NEO006 435480.1333 1.0 -7470490.0816 8341450.3483 False BAS NEO2 625424.9333 1.0 -7280545.2816 8531395.1483 False BAS PBS 623998.2 1.0 -4966366.9509 6214363.3509 False BAS REB 310270.5333 1.0 -7595699.6816 8216240.7483 False BAS SAA 1723787.7333 1.0 -6182182.4816 9629757.9483 False BAS SAC05 140954.9333 1.0 -7765015.2816 8046925.1483 False BAS SAC2 375052.1333 1.0 -7530918.0816 8281022.3483 False BAS SOR 1035688.4667 1.0 -4554676.6842 6626053.6175 False BAS STE -295299.0667 1.0 -8201269.2816 7610671.1483 False BAS SUC 886222.7333 1.0 -7019747.4816 8792192.9483 False BAS THA03 847865.9333 1.0 -7058104.2816 8753836.1483 False BAS THA2 951470.9333 1.0 -6954499.2816 8857441.1483 False BAS XYL 1649733.3333 1.0 -6256236.8816 9555703.5483 False CYC ERY 791368.0 1.0 -8891428.4742 10474164.4742 False CYC FOS 716356.2 1.0 -8966440.2742 10399152.6742 False CYC GLU 1375124.6 1.0 -8307671.8742 11057921.0742 False CYC HSH 10071489.8 0.0304 388693.3258 19754286.2742 True CYC ISO 27755726.6 0.0 18072930.1258 37438523.0742 True CYC KES 332924.0 1.0 -9349872.4742 10015720.4742 False CYC LAC -202143.8 1.0 -9884940.2742 9480652.6742 False CYC MAL 33924567.8 0.0 24241771.3258 43607364.2742 True CYC MAN -147912.0 1.0 -8053882.215 7758058.215 False CYC MFE -1354392.4 1.0 -11037188.8742 8328404.0742 False CYC NDC -542171.4 1.0 -10224967.8742 9140625.0742 False CYC NEO006 -457748.6 1.0 -10140545.0742 9225047.8742 False CYC NEO2 -267803.8 1.0 -9950600.2742 9414992.6742 False CYC PBS -269230.5333 1.0 -8175200.7483 7636739.6816 False CYC REB -582958.2 1.0 -10265754.6742 9099838.2742 False CYC SAA 830559.0 1.0 -8852237.4742 10513355.4742 False CYC SAC05 -752273.8 1.0 -10435070.2742 8930522.6742 False CYC SAC2 -518176.6 1.0 -10200973.0742 9164619.8742 False CYC SOR 142459.7333 1.0 -7763510.4816 8048429.9483 False CYC STE -1188527.8 1.0 -10871324.2742 8494268.6742 False CYC SUC -7006.0 1.0 -9689802.4742 9675790.4742 False CYC THA03 -45362.8 1.0 -9728159.2742 9637433.6742 False CYC THA2 58242.2 1.0 -9624554.2742 9741038.6742 False CYC XYL 756504.6 1.0 -8926291.8742 10439301.0742 False ERY FOS -75011.8 1.0 -9757808.2742 9607784.6742 False ERY GLU 583756.6 1.0 -9099039.8742 10266553.0742 False ERY HSH 9280121.8 0.081 -402674.6742 18962918.2742 False ERY ISO 26964358.6 0.0 17281562.1258 36647155.0742 True ERY KES -458444.0 1.0 -10141240.4742 9224352.4742 False ERY LAC -993511.8 1.0 -10676308.2742 8689284.6742 False ERY MAL 33133199.8 0.0 23450403.3258 42815996.2742 True ERY MAN -939280.0 1.0 -8845250.215 6966690.215 False ERY MFE -2145760.4 1.0 -11828556.8742 7537036.0742 False ERY NDC -1333539.4 1.0 -11016335.8742 8349257.0742 False ERY NEO006 -1249116.6 1.0 -10931913.0742 8433679.8742 False ERY NEO2 -1059171.8 1.0 -10741968.2742 8623624.6742 False ERY PBS -1060598.5333 1.0 -8966568.7483 6845371.6816 False ERY REB -1374326.2 1.0 -11057122.6742 8308470.2742 False ERY SAA 39191.0 1.0 -9643605.4742 9721987.4742 False ERY SAC05 -1543641.8 1.0 -11226438.2742 8139154.6742 False ERY SAC2 -1309544.6 1.0 -10992341.0742 8373251.8742 False ERY SOR -648908.2667 1.0 -8554878.4816 7257061.9483 False ERY STE -1979895.8 1.0 -11662692.2742 7702900.6742 False ERY SUC -798374.0 1.0 -10481170.4742 8884422.4742 False ERY THA03 -836730.8 1.0 -10519527.2742 8846065.6742 False ERY THA2 -733125.8 1.0 -10415922.2742 8949670.6742 False ERY XYL -34863.4 1.0 -9717659.8742 9647933.0742 False FOS GLU 658768.4 1.0 -9024028.0742 10341564.8742 False FOS HSH 9355133.6 0.0742 -327662.8742 19037930.0742 False FOS ISO 27039370.4 0.0 17356573.9258 36722166.8742 True FOS KES -383432.2 1.0 -10066228.6742 9299364.2742 False FOS LAC -918500.0 1.0 -10601296.4742 8764296.4742 False FOS MAL 33208211.6 0.0 23525415.1258 42891008.0742 True FOS MAN -864268.2 1.0 -8770238.415 7041702.015 False FOS MFE -2070748.6 1.0 -11753545.0742 7612047.8742 False FOS NDC -1258527.6 1.0 -10941324.0742 8424268.8742 False FOS NEO006 -1174104.8 1.0 -10856901.2742 8508691.6742 False FOS NEO2 -984160.0 1.0 -10666956.4742 8698636.4742 False FOS PBS -985586.7333 1.0 -8891556.9483 6920383.4816 False FOS REB -1299314.4 1.0 -10982110.8742 8383482.0742 False FOS SAA 114202.8 1.0 -9568593.6742 9796999.2742 False FOS SAC05 -1468630.0 1.0 -11151426.4742 8214166.4742 False FOS SAC2 -1234532.8 1.0 -10917329.2742 8448263.6742 False FOS SOR -573896.4667 1.0 -8479866.6816 7332073.7483 False FOS STE -1904884.0 1.0 -11587680.4742 7777912.4742 False FOS SUC -723362.2 1.0 -10406158.6742 8959434.2742 False FOS THA03 -761719.0 1.0 -10444515.4742 8921077.4742 False FOS THA2 -658114.0 1.0 -10340910.4742 9024682.4742 False FOS XYL 40148.4 1.0 -9642648.0742 9722944.8742 False GLU HSH 8696365.2 0.1528 -986431.2742 18379161.6742 False GLU ISO 26380602.0 0.0 16697805.5258 36063398.4742 True GLU KES -1042200.6 1.0 -10724997.0742 8640595.8742 False GLU LAC -1577268.4 1.0 -11260064.8742 8105528.0742 False GLU MAL 32549443.2 0.0 22866646.7258 42232239.6742 True GLU MAN -1523036.6 1.0 -9429006.815 6382933.615 False GLU MFE -2729517.0 1.0 -12412313.4742 6953279.4742 False GLU NDC -1917296.0 1.0 -11600092.4742 7765500.4742 False GLU NEO006 -1832873.2 1.0 -11515669.6742 7849923.2742 False GLU NEO2 -1642928.4 1.0 -11325724.8742 8039868.0742 False GLU PBS -1644355.1333 1.0 -9550325.3483 6261615.0816 False GLU REB -1958082.8 1.0 -11640879.2742 7724713.6742 False GLU SAA -544565.6 1.0 -10227362.0742 9138230.8742 False GLU SAC05 -2127398.4 1.0 -11810194.8742 7555398.0742 False GLU SAC2 -1893301.2 1.0 -11576097.6742 7789495.2742 False GLU SOR -1232664.8667 1.0 -9138635.0816 6673305.3483 False GLU STE -2563652.4 1.0 -12246448.8742 7119144.0742 False GLU SUC -1382130.6 1.0 -11064927.0742 8300665.8742 False GLU THA03 -1420487.4 1.0 -11103283.8742 8262309.0742 False GLU THA2 -1316882.4 1.0 -10999678.8742 8365914.0742 False GLU XYL -618620.0 1.0 -10301416.4742 9064176.4742 False HSH ISO 17684236.8 0.0 8001440.3258 27367033.2742 True HSH KES -9738565.8 0.0466 -19421362.2742 -55769.3258 True HSH LAC -10273633.6 0.0232 -19956430.0742 -590837.1258 True HSH MAL 23853078.0 0.0 14170281.5258 33535874.4742 True HSH MAN -10219401.8 0.0008 -18125372.015 -2313431.585 True HSH MFE -11425882.2 0.0044 -21108678.6742 -1743085.7258 True HSH NDC -10613661.2 0.0145 -20296457.6742 -930864.7258 True HSH NEO006 -10529238.4 0.0163 -20212034.8742 -846441.9258 True HSH NEO2 -10339293.6 0.0213 -20022090.0742 -656497.1258 True HSH PBS -10340720.3333 0.0006 -18246690.5483 -2434750.1184 True HSH REB -10654448.0 0.0137 -20337244.4742 -971651.5258 True HSH SAA -9240930.8 0.0847 -18923727.2742 441865.6742 False HSH SAC05 -10823763.6 0.0108 -20506560.0742 -1140967.1258 True HSH SAC2 -10589666.4 0.015 -20272462.8742 -906869.9258 True HSH SOR -9929030.0667 0.0014 -17835000.2816 -2023059.8517 True HSH STE -11260017.6 0.0056 -20942814.0742 -1577221.1258 True HSH SUC -10078495.8 0.0301 -19761292.2742 -395699.3258 True HSH THA03 -10116852.6 0.0287 -19799649.0742 -434056.1258 True HSH THA2 -10013247.6 0.0328 -19696044.0742 -330451.1258 True HSH XYL -9314985.2 0.0778 -18997781.6742 367811.2742 False ISO KES -27422802.6 0.0 -37105599.0742 -17740006.1258 True ISO LAC -27957870.4 0.0 -37640666.8742 -18275073.9258 True ISO MAL 6168841.2 0.8168 -3513955.2742 15851637.6742 False ISO MAN -27903638.6 0.0 -35809608.815 -19997668.385 True ISO MFE -29110119.0 0.0 -38792915.4742 -19427322.5258 True ISO NDC -28297898.0 0.0 -37980694.4742 -18615101.5258 True ISO NEO006 -28213475.2 0.0 -37896271.6742 -18530678.7258 True ISO NEO2 -28023530.4 0.0 -37706326.8742 -18340733.9258 True ISO PBS -28024957.1333 0.0 -35930927.3483 -20118986.9184 True ISO REB -28338684.8 0.0 -38021481.2742 -18655888.3258 True ISO SAA -26925167.6 0.0 -36607964.0742 -17242371.1258 True ISO SAC05 -28508000.4 0.0 -38190796.8742 -18825203.9258 True ISO SAC2 -28273903.2 0.0 -37956699.6742 -18591106.7258 True ISO SOR -27613266.8667 0.0 -35519237.0816 -19707296.6517 True ISO STE -28944254.4 0.0 -38627050.8742 -19261457.9258 True ISO SUC -27762732.6 0.0 -37445529.0742 -18079936.1258 True ISO THA03 -27801089.4 0.0 -37483885.8742 -18118292.9258 True ISO THA2 -27697484.4 0.0 -37380280.8742 -18014687.9258 True ISO XYL -26999222.0 0.0 -36682018.4742 -17316425.5258 True KES LAC -535067.8 1.0 -10217864.2742 9147728.6742 False KES MAL 33591643.8 0.0 23908847.3258 43274440.2742 True KES MAN -480836.0 1.0 -8386806.215 7425134.215 False KES MFE -1687316.4 1.0 -11370112.8742 7995480.0742 False KES NDC -875095.4 1.0 -10557891.8742 8807701.0742 False KES NEO006 -790672.6 1.0 -10473469.0742 8892123.8742 False KES NEO2 -600727.8 1.0 -10283524.2742 9082068.6742 False KES PBS -602154.5333 1.0 -8508124.7483 7303815.6816 False KES REB -915882.2 1.0 -10598678.6742 8766914.2742 False KES SAA 497635.0 1.0 -9185161.4742 10180431.4742 False KES SAC05 -1085197.8 1.0 -10767994.2742 8597598.6742 False KES SAC2 -851100.6 1.0 -10533897.0742 8831695.8742 False KES SOR -190464.2667 1.0 -8096434.4816 7715505.9483 False KES STE -1521451.8 1.0 -11204248.2742 8161344.6742 False KES SUC -339930.0 1.0 -10022726.4742 9342866.4742 False KES THA03 -378286.8 1.0 -10061083.2742 9304509.6742 False KES THA2 -274681.8 1.0 -9957478.2742 9408114.6742 False KES XYL 423580.6 1.0 -9259215.8742 10106377.0742 False LAC MAL 34126711.6 0.0 24443915.1258 43809508.0742 True LAC MAN 54231.8 1.0 -7851738.415 7960202.015 False LAC MFE -1152248.6 1.0 -10835045.0742 8530547.8742 False LAC NDC -340027.6 1.0 -10022824.0742 9342768.8742 False LAC NEO006 -255604.8 1.0 -9938401.2742 9427191.6742 False LAC NEO2 -65660.0 1.0 -9748456.4742 9617136.4742 False LAC PBS -67086.7333 1.0 -7973056.9483 7838883.4816 False LAC REB -380814.4 1.0 -10063610.8742 9301982.0742 False LAC SAA 1032702.8 1.0 -8650093.6742 10715499.2742 False LAC SAC05 -550130.0 1.0 -10232926.4742 9132666.4742 False LAC SAC2 -316032.8 1.0 -9998829.2742 9366763.6742 False LAC SOR 344603.5333 1.0 -7561366.6816 8250573.7483 False LAC STE -986384.0 1.0 -10669180.4742 8696412.4742 False LAC SUC 195137.8 1.0 -9487658.6742 9877934.2742 False LAC THA03 156781.0 1.0 -9526015.4742 9839577.4742 False LAC THA2 260386.0 1.0 -9422410.4742 9943182.4742 False LAC XYL 958648.4 1.0 -8724148.0742 10641444.8742 False MAL MAN -34072479.8 0.0 -41978450.015 -26166509.585 True MAL MFE -35278960.2 0.0 -44961756.6742 -25596163.7258 True MAL NDC -34466739.2 0.0 -44149535.6742 -24783942.7258 True MAL NEO006 -34382316.4 0.0 -44065112.8742 -24699519.9258 True MAL NEO2 -34192371.6 0.0 -43875168.0742 -24509575.1258 True MAL PBS -34193798.3333 0.0 -42099768.5483 -26287828.1184 True MAL REB -34507526.0 0.0 -44190322.4742 -24824729.5258 True MAL SAA -33094008.8 0.0 -42776805.2742 -23411212.3258 True MAL SAC05 -34676841.6 0.0 -44359638.0742 -24994045.1258 True MAL SAC2 -34442744.4 0.0 -44125540.8742 -24759947.9258 True MAL SOR -33782108.0667 0.0 -41688078.2816 -25876137.8517 True MAL STE -35113095.6 0.0 -44795892.0742 -25430299.1258 True MAL SUC -33931573.8 0.0 -43614370.2742 -24248777.3258 True MAL THA03 -33969930.6 0.0 -43652727.0742 -24287134.1258 True MAL THA2 -33866325.6 0.0 -43549122.0742 -24183529.1258 True MAL XYL -33168063.2 0.0 -42850859.6742 -23485266.7258 True MAN MFE -1206480.4 1.0 -9112450.615 6699489.815 False MAN NDC -394259.4 1.0 -8300229.615 7511710.815 False MAN NEO006 -309836.6 1.0 -8215806.815 7596133.615 False MAN NEO2 -119891.8 1.0 -8025862.015 7786078.415 False MAN PBS -121318.5333 1.0 -5711683.6842 5469046.6175 False MAN REB -435046.2 1.0 -8341016.415 7470924.015 False MAN SAA 978471.0 1.0 -6927499.215 8884441.215 False MAN SAC05 -604361.8 1.0 -8510332.015 7301608.415 False MAN SAC2 -370264.6 1.0 -8276234.815 7535705.615 False MAN SOR 290371.7333 1.0 -5299993.4175 5880736.8842 False MAN STE -1040615.8 1.0 -8946586.015 6865354.415 False MAN SUC 140906.0 1.0 -7765064.215 8046876.215 False MAN THA03 102549.2 1.0 -7803421.015 8008519.415 False MAN THA2 206154.2 1.0 -7699816.015 8112124.415 False MAN XYL 904416.6 1.0 -7001553.615 8810386.815 False MFE NDC 812221.0 1.0 -8870575.4742 10495017.4742 False MFE NEO006 896643.8 1.0 -8786152.6742 10579440.2742 False MFE NEO2 1086588.6 1.0 -8596207.8742 10769385.0742 False MFE PBS 1085161.8667 1.0 -6820808.3483 8991132.0816 False MFE REB 771434.2 1.0 -8911362.2742 10454230.6742 False MFE SAA 2184951.4 1.0 -7497845.0742 11867747.8742 False MFE SAC05 602118.6 1.0 -9080677.8742 10284915.0742 False MFE SAC2 836215.8 1.0 -8846580.6742 10519012.2742 False MFE SOR 1496852.1333 1.0 -6409118.0816 9402822.3483 False MFE STE 165864.6 1.0 -9516931.8742 9848661.0742 False MFE SUC 1347386.4 1.0 -8335410.0742 11030182.8742 False MFE THA03 1309029.6 1.0 -8373766.8742 10991826.0742 False MFE THA2 1412634.6 1.0 -8270161.8742 11095431.0742 False MFE XYL 2110897.0 1.0 -7571899.4742 11793693.4742 False NDC NEO006 84422.8 1.0 -9598373.6742 9767219.2742 False NDC NEO2 274367.6 1.0 -9408428.8742 9957164.0742 False NDC PBS 272940.8667 1.0 -7633029.3483 8178911.0816 False NDC REB -40786.8 1.0 -9723583.2742 9642009.6742 False NDC SAA 1372730.4 1.0 -8310066.0742 11055526.8742 False NDC SAC05 -210102.4 1.0 -9892898.8742 9472694.0742 False NDC SAC2 23994.8 1.0 -9658801.6742 9706791.2742 False NDC SOR 684631.1333 1.0 -7221339.0816 8590601.3483 False NDC STE -646356.4 1.0 -10329152.8742 9036440.0742 False NDC SUC 535165.4 1.0 -9147631.0742 10217961.8742 False NDC THA03 496808.6 1.0 -9185987.8742 10179605.0742 False NDC THA2 600413.6 1.0 -9082382.8742 10283210.0742 False NDC XYL 1298676.0 1.0 -8384120.4742 10981472.4742 False NEO006 NEO2 189944.8 1.0 -9492851.6742 9872741.2742 False NEO006 PBS 188518.0667 1.0 -7717452.1483 8094488.2816 False NEO006 REB -125209.6 1.0 -9808006.0742 9557586.8742 False NEO006 SAA 1288307.6 1.0 -8394488.8742 10971104.0742 False NEO006 SAC05 -294525.2 1.0 -9977321.6742 9388271.2742 False NEO006 SAC2 -60428.0 1.0 -9743224.4742 9622368.4742 False NEO006 SOR 600208.3333 1.0 -7305761.8816 8506178.5483 False NEO006 STE -730779.2 1.0 -10413575.6742 8952017.2742 False NEO006 SUC 450742.6 1.0 -9232053.8742 10133539.0742 False NEO006 THA03 412385.8 1.0 -9270410.6742 10095182.2742 False NEO006 THA2 515990.8 1.0 -9166805.6742 10198787.2742 False NEO006 XYL 1214253.2 1.0 -8468543.2742 10897049.6742 False NEO2 PBS -1426.7333 1.0 -7907396.9483 7904543.4816 False NEO2 REB -315154.4 1.0 -9997950.8742 9367642.0742 False NEO2 SAA 1098362.8 1.0 -8584433.6742 10781159.2742 False NEO2 SAC05 -484470.0 1.0 -10167266.4742 9198326.4742 False NEO2 SAC2 -250372.8 1.0 -9933169.2742 9432423.6742 False NEO2 SOR 410263.5333 1.0 -7495706.6816 8316233.7483 False NEO2 STE -920724.0 1.0 -10603520.4742 8762072.4742 False NEO2 SUC 260797.8 1.0 -9421998.6742 9943594.2742 False NEO2 THA03 222441.0 1.0 -9460355.4742 9905237.4742 False NEO2 THA2 326046.0 1.0 -9356750.4742 10008842.4742 False NEO2 XYL 1024308.4 1.0 -8658488.0742 10707104.8742 False PBS REB -313727.6667 1.0 -8219697.8816 7592242.5483 False PBS SAA 1099789.5333 1.0 -6806180.6816 9005759.7483 False PBS SAC05 -483043.2667 1.0 -8389013.4816 7422926.9483 False PBS SAC2 -248946.0667 1.0 -8154916.2816 7657024.1483 False PBS SOR 411690.2667 1.0 -5178674.8842 6002055.4175 False PBS STE -919297.2667 1.0 -8825267.4816 6986672.9483 False PBS SUC 262224.5333 1.0 -7643745.6816 8168194.7483 False PBS THA03 223867.7333 1.0 -7682102.4816 8129837.9483 False PBS THA2 327472.7333 1.0 -7578497.4816 8233442.9483 False PBS XYL 1025735.1333 1.0 -6880235.0816 8931705.3483 False REB SAA 1413517.2 1.0 -8269279.2742 11096313.6742 False REB SAC05 -169315.6 1.0 -9852112.0742 9513480.8742 False REB SAC2 64781.6 1.0 -9618014.8742 9747578.0742 False REB SOR 725417.9333 1.0 -7180552.2816 8631388.1483 False REB STE -605569.6 1.0 -10288366.0742 9077226.8742 False REB SUC 575952.2 1.0 -9106844.2742 10258748.6742 False REB THA03 537595.4 1.0 -9145201.0742 10220391.8742 False REB THA2 641200.4 1.0 -9041596.0742 10323996.8742 False REB XYL 1339462.8 1.0 -8343333.6742 11022259.2742 False SAA SAC05 -1582832.8 1.0 -11265629.2742 8099963.6742 False SAA SAC2 -1348735.6 1.0 -11031532.0742 8334060.8742 False SAA SOR -688099.2667 1.0 -8594069.4816 7217870.9483 False SAA STE -2019086.8 1.0 -11701883.2742 7663709.6742 False SAA SUC -837565.0 1.0 -10520361.4742 8845231.4742 False SAA THA03 -875921.8 1.0 -10558718.2742 8806874.6742 False SAA THA2 -772316.8 1.0 -10455113.2742 8910479.6742 False SAA XYL -74054.4 1.0 -9756850.8742 9608742.0742 False SAC05 SAC2 234097.2 1.0 -9448699.2742 9916893.6742 False SAC05 SOR 894733.5333 1.0 -7011236.6816 8800703.7483 False SAC05 STE -436254.0 1.0 -10119050.4742 9246542.4742 False SAC05 SUC 745267.8 1.0 -8937528.6742 10428064.2742 False SAC05 THA03 706911.0 1.0 -8975885.4742 10389707.4742 False SAC05 THA2 810516.0 1.0 -8872280.4742 10493312.4742 False SAC05 XYL 1508778.4 1.0 -8174018.0742 11191574.8742 False SAC2 SOR 660636.3333 1.0 -7245333.8816 8566606.5483 False SAC2 STE -670351.2 1.0 -10353147.6742 9012445.2742 False SAC2 SUC 511170.6 1.0 -9171625.8742 10193967.0742 False SAC2 THA03 472813.8 1.0 -9209982.6742 10155610.2742 False SAC2 THA2 576418.8 1.0 -9106377.6742 10259215.2742 False SAC2 XYL 1274681.2 1.0 -8408115.2742 10957477.6742 False SOR STE -1330987.5333 1.0 -9236957.7483 6574982.6816 False SOR SUC -149465.7333 1.0 -8055435.9483 7756504.4816 False SOR THA03 -187822.5333 1.0 -8093792.7483 7718147.6816 False SOR THA2 -84217.5333 1.0 -7990187.7483 7821752.6816 False SOR XYL 614044.8667 1.0 -7291925.3483 8520015.0816 False STE SUC 1181521.8 1.0 -8501274.6742 10864318.2742 False STE THA03 1143165.0 1.0 -8539631.4742 10825961.4742 False STE THA2 1246770.0 1.0 -8436026.4742 10929566.4742 False STE XYL 1945032.4 1.0 -7737764.0742 11627828.8742 False SUC THA03 -38356.8 1.0 -9721153.2742 9644439.6742 False SUC THA2 65248.2 1.0 -9617548.2742 9748044.6742 False SUC XYL 763510.6 1.0 -8919285.8742 10446307.0742 False THA03 THA2 103605.0 1.0 -9579191.4742 9786401.4742 False THA03 XYL 801867.4 1.0 -8880929.0742 10484663.8742 False THA2 XYL 698262.4 1.0 -8984534.0742 10381058.8742 False ------------------------------------------------------------------------
tp = TukeyPlot()
tp.plot_tukey(df_tukey)
<Axes: title={'center': 'The Tukey test result'}, xlabel='The difference of mean value', ylabel='Groups'>
df_ttest = sw.get_stats_ttest(group_list=['MAL', 'PBS'])
display(df_ttest.sort_values(by='P-value'))
t-test for Taxon-Description in ['MAL', 'PBS']
100%|██████████| 20739/20739 [00:33<00:00, 614.41it/s]
| P-value | t-statistic | V1_32 | V2_32 | V3_32 | V4_32 | V5_32 | V1_01 | V1_26 | V1_37 | ... | V2_37 | V3_01 | V3_26 | V3_37 | V4_01 | V4_26 | V4_37 | V5_01 | V5_26 | V5_37 | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Taxon | Description | |||||||||||||||||||||
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A | Belongs to the bacterial ribosomal protein bS16 family | 6.530428e-11 | 13.604118 | 3405147 | 2031408 | 3890510 | 3174528 | 3735839 | 495699 | 618303 | 0 | ... | 0 | 0 | 606541 | 0 | 377076 | 0 | 0 | 0 | 408600 | 0 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A massiliensis | Belongs to the phosphoglycerate kinase family | 1.422027e-10 | 12.974279 | 10544927 | 7925416 | 12979505 | 8669368 | 10268308 | 2376259 | 2298544 | 2032377 | ... | 3021435 | 2468879 | 2453278 | 1687110 | 3090003 | 1835245 | 3525475 | 2499385 | 1936377 | 1649894 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A | Putative cell wall binding repeat | 5.536336e-10 | 11.931107 | 4024996 | 2184018 | 2897185 | 3198223 | 3172044 | 467096 | 0 | 290105 | ... | 364883 | 606735 | 0 | 618545 | 244241 | 441393 | 63637 | 481833 | 142226 | 870203 |
| Bacterial extracellular solute-binding protein | 6.026885e-10 | 11.868243 | 55357633 | 38368403 | 69739326 | 37982563 | 64018487 | 10357237 | 5822630 | 9279453 | ... | 9029598 | 10329806 | 12966514 | 9913544 | 5018059 | 3957163 | 2260259 | 7135096 | 5804131 | 9991801 | |
| Psort location Cytoplasmic, score 9.98 | 8.880045e-09 | 10.003715 | 33008066 | 62835342 | 53925379 | 41611821 | 70276260 | 16946312 | 16233511 | 10743316 | ... | 13545490 | 15380275 | 11562475 | 13704287 | 16578006 | 8585544 | 11287176 | 15287787 | 16077613 | 12603490 | |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila_A | Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin | NaN | NaN | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp004167605 | Glycoside hydrolase, family 20, catalytic core | NaN | NaN | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine | NaN | NaN | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp900766865 | Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome | NaN | NaN | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Pyruvate phosphate dikinase, PEP/pyruvate binding domain | NaN | NaN | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
20739 rows × 22 columns
hp.plot_top_taxa_func_heatmap_of_test_res(df_ttest, sw.func, 100, 'p')
Table size: 20739 x 22 Recommended figure size: width: 27, length: 40, front_title: 20, font_size: 10
<seaborn.matrix.ClusterGrid at 0x187829e3e20>
df_fc = sw.get_stats_deseq2(sw.taxa_func_df , group_list=['MAL', 'PBS'])
Fitting size factors... ... done in 0.02 seconds. Fitting dispersions... ... done in 3.63 seconds. Fitting dispersion trend curve... ... done in 5.58 seconds. Fitting MAP dispersions... ... done in 3.45 seconds. Fitting LFCs... ... done in 8.65 seconds. Refitting 5499 outliers. Fitting dispersions... ... done in 0.69 seconds. Fitting MAP dispersions... ... done in 0.59 seconds. Fitting LFCs... ... done in 4.27 seconds. Running Wald tests... ... done in 1.52 seconds. Log2 fold change & Wald test p-value: Sweetener PBS vs MAL
| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
|---|---|---|---|---|---|---|
| Taxa-Func | ||||||
| d__Archaea|p__Halobacteriota|c__Halobacteria|o__Halobacteriales|f__Haloferacaceae|g__Haloferax|s__Haloferax massiliensis [Electron transfer flavoprotein, beta subunit] | 0.000000 | NaN | NaN | NaN | NaN | NaN |
| d__Archaea|p__Halobacteriota|c__Halobacteria|o__Halobacteriales|f__Haloferacaceae|g__Haloferax|s__Haloferax massiliensis [Involved in regulation of DNA replication] | 7328.721114 | -0.337907 | 2.304200 | -0.146648 | 0.883410 | 0.999902 |
| d__Archaea|p__Halobacteriota|c__Halobacteria|o__Halobacteriales|f__Haloferacaceae|g__Haloferax|s__Haloferax massiliensis [NADH ubiquinone oxidoreductase subunit 1 (Chain H)] | 0.000000 | NaN | NaN | NaN | NaN | NaN |
| d__Archaea|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobacterium|s__Methanobacterium sp000499765 [Binds directly to 23S rRNA. Probably involved in E site tRNA release] | 4244.426286 | -4.409273 | 3.331767 | -1.323403 | NaN | NaN |
| d__Archaea|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobacterium|s__Methanobacterium sp000499765 [Molecular chaperone capable of stabilizing a range of proteins. Seems to fulfill an ATP-independent, HSP70-like function in archaeal de novo protein folding] | 0.000000 | NaN | NaN | NaN | NaN | NaN |
| ... | ... | ... | ... | ... | ... | ... |
| d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp004167605 [Prevents misfolding and promotes the refolding and proper assembly of unfolded polypeptides generated under stress conditions] | 6156.085578 | 0.017438 | 0.963073 | 0.018107 | 0.985554 | 0.999902 |
| d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp004167605 [carbohydrate kinase activity] | 2124.127616 | -0.167809 | 2.660427 | -0.063076 | 0.949706 | 0.999902 |
| d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp004167605 [outer membrane autotransporter barrel domain protein] | 162.398547 | 8.914786 | 0.000000 | 0.000000 | NaN | NaN |
| d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp900766865 [Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome] | 0.000000 | NaN | NaN | NaN | NaN | NaN |
| d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp900766865 [Pyruvate phosphate dikinase, PEP/pyruvate binding domain] | 0.000000 | NaN | NaN | NaN | NaN | NaN |
20739 rows × 6 columns
padj and log2FoldChangedisplay(df_fc.sort_values(by=['padj', 'log2FoldChange']))
| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | V1_32 | V2_32 | V3_32 | V4_32 | ... | V2_37 | V3_01 | V3_26 | V3_37 | V4_01 | V4_26 | V4_37 | V5_01 | V5_26 | V5_37 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Taxa-Func | |||||||||||||||||||||
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Alpha amylase catalytic] | 125962.524088 | -3.348493 | 0.379603 | -8.821037 | 1.134047e-18 | 1.579274e-14 | 20316636 | 27951767 | 45648544 | 28992727 | ... | 3550704 | 5603981 | 5221565 | 6940798 | 4124013 | 2674402 | 4526463 | 2119099 | 2277697 | 2426268 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Psort location Cytoplasmic, score 9.98] | 233511.214560 | -1.973048 | 0.257091 | -7.674504 | 1.660605e-14 | 1.156279e-10 | 33008066 | 62835342 | 53925379 | 41611821 | ... | 13545490 | 15380275 | 11562475 | 13704287 | 16578006 | 8585544 | 11287176 | 15287787 | 16077613 | 12603490 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [D-isomer specific 2-hydroxyacid dehydrogenase] | 1918.011025 | -15.361539 | 2.024428 | -7.588090 | 3.246559e-14 | 1.507052e-10 | 1264470 | 157859 | 523497 | 219077 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Bacterial extracellular solute-binding protein] | 194107.642804 | -2.768583 | 0.369716 | -7.488398 | 6.971951e-14 | 2.427285e-10 | 55357633 | 38368403 | 69739326 | 37982563 | ... | 9029598 | 10329806 | 12966514 | 9913544 | 5018059 | 3957163 | 2260259 | 7135096 | 5804131 | 9991801 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit] | 38199.451975 | -2.881334 | 0.401324 | -7.179569 | 6.993161e-13 | 1.725167e-09 | 7711614 | 6443415 | 12765501 | 8050715 | ... | 1319253 | 1887998 | 1882542 | 1700035 | 1292280 | 1040357 | 328831 | 1746933 | 2588074 | 1509087 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila_A [Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin] | 0.000000 | NaN | NaN | NaN | NaN | NaN | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp004167605 [Glycoside hydrolase, family 20, catalytic core] | 0.000000 | NaN | NaN | NaN | NaN | NaN | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp004167605 [May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine] | 0.000000 | NaN | NaN | NaN | NaN | NaN | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp900766865 [Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome] | 0.000000 | NaN | NaN | NaN | NaN | NaN | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| d__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp900766865 [Pyruvate phosphate dikinase, PEP/pyruvate binding domain] | 0.000000 | NaN | NaN | NaN | NaN | NaN | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
20739 rows × 26 columns
padj=0.05, log2fc=1vp = VolcanoPlot()
vp.plot_volcano(df = df_fc, padj=0.05, log2fc=1, title_name='NDC vs BAS', figsize=(8, 6))
<Axes: title={'center': 'Volcano plot of NDC vs BAS (padj < 0.05, log2FoldChange > 1)'}, xlabel='log2FoldChange', ylabel='-log10(padj)'>
width=1200, height=800, p_value=0.005, log2fc=1sp = SankeyPlot()
pic = sp.plot_fc_sankey(df_fc, width=1200, height=800, p_value=0.005, log2fc=1)
pic.render_notebook()
Creating nodes and links for upregulated... Number of nodes: 101 Number of links: 102 Creating nodes and links for downregulated... Number of nodes: 70 Number of links: 69
Input: a group nameoutput: a list containing all samples of the groupsw.get_sample_list_in_a_group('NDC')
['V1_17', 'V2_17', 'V3_17', 'V4_17', 'V5_17']
Input: a meat nameoutput: a list containing all groups of the metaprint(sw.get_meta_list('Person'))
['V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V1', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V2', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V3', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V4', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5', 'V5']
taxon = 'd__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A'
function = 'Alpha amylase catalytic'
Input: a taxon nameoutput: A matrix of all functional intensity under the taxonsw.get_intensity_matrix(taxon_name=taxon)
| V1_01 | V1_02 | V1_03 | V1_04 | V1_05 | V1_06 | V1_07 | V1_08 | V1_09 | V1_10 | ... | V5_29 | V5_30 | V5_31 | V5_32 | V5_33 | V5_34 | V5_35 | V5_36 | V5_37 | V5_38 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Description | |||||||||||||||||||||
| 4Fe-4S dicluster domain | 0 | 2615194 | 862507 | 0 | 1657281 | 0 | 0 | 202091 | 0 | 306054 | ... | 0 | 0 | 4359213 | 3974126 | 7630749 | 0 | 0 | 0 | 0 | 2036744 |
| ABC transporter substrate binding protein | 399325 | 0 | 0 | 554314 | 0 | 0 | 0 | 276083 | 454484 | 282606 | ... | 279801 | 241201 | 0 | 232880 | 0 | 0 | 354653 | 166981 | 203408 | 181204 |
| ABC transporter substrate-binding protein PnrA-like | 4801530 | 8214579 | 6014136 | 2932604 | 8927618 | 5693465 | 2612510 | 6079875 | 3840413 | 7112622 | ... | 4873780 | 2538617 | 6119082 | 10595852 | 8602937 | 4140661 | 2924249 | 3492467 | 1995332 | 6695263 |
| ABC transporter, solute-binding protein | 68697 | 1926695 | 538352 | 782061 | 707150 | 558362 | 927291 | 159072 | 2955851 | 894248 | ... | 5423611 | 0 | 0 | 0 | 491801 | 0 | 0 | 0 | 0 | 0 |
| ABC-type branched-chain amino acid transport systems periplasmic component | 142014 | 388602 | 0 | 0 | 233492 | 0 | 0 | 107147 | 0 | 0 | ... | 0 | 0 | 151530 | 0 | 0 | 440469 | 0 | 0 | 0 | 0 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| phenylalanyl-tRNA synthetase (beta subunit) | 558425 | 2291605 | 1047544 | 622633 | 2117798 | 215328 | 201782 | 444547 | 531796 | 1047894 | ... | 603772 | 579479 | 2748865 | 4276744 | 3160508 | 222057 | 411237 | 0 | 737657 | 1135023 |
| precorrin-4 C11-methyltransferase | 614252 | 772312 | 0 | 1342845 | 725014 | 580376 | 0 | 846369 | 1547419 | 0 | ... | 0 | 0 | 0 | 1481962 | 1017100 | 0 | 0 | 0 | 0 | 0 |
| self proteolysis | 7835853 | 3782073 | 2542271 | 6115328 | 5946785 | 5431637 | 2889251 | 3079824 | 3154294 | 7071532 | ... | 2908560 | 5384647 | 22813316 | 29091793 | 15613756 | 4346420 | 3843680 | 2131130 | 3034220 | 22607359 |
| translation elongation factor G | 3437430 | 22621869 | 8663979 | 1737353 | 8453812 | 2728469 | 2370272 | 5187042 | 3487809 | 5787783 | ... | 2689900 | 2391601 | 7891932 | 17890371 | 18866048 | 1862133 | 1987872 | 2038818 | 2275986 | 9101159 |
| transport systems ATPase components | 573759 | 502586 | 328627 | 216013 | 853016 | 0 | 0 | 340364 | 244512 | 459331 | ... | 0 | 1030323 | 313082 | 517430 | 933291 | 0 | 559629 | 550918 | 313763 | 0 |
231 rows × 190 columns
Input: a function nameoutput: A matrix of all species intensity under the functionsw.get_intensity_matrix(func_name=function)
| V1_01 | V1_02 | V1_03 | V1_04 | V1_05 | V1_06 | V1_07 | V1_08 | V1_09 | V1_10 | ... | V5_29 | V5_30 | V5_31 | V5_32 | V5_33 | V5_34 | V5_35 | V5_36 | V5_37 | V5_38 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Taxon | |||||||||||||||||||||
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A luti | 0 | 1695192 | 0 | 0 | 1625777 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A sp003477525 | 619484 | 2817471 | 710294 | 504574 | 2518867 | 462228 | 538816 | 302569 | 341525 | 600846 | ... | 255284 | 0 | 0 | 3601729 | 0 | 104086 | 0 | 0 | 0 | 0 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A | 3571092 | 15314463 | 4256180 | 3090474 | 14250829 | 3958464 | 2138617 | 5030109 | 3282561 | 3785770 | ... | 5417808 | 1477560 | 5192762 | 67409590 | 6813235 | 3972182 | 2838313 | 3006783 | 2426268 | 3675044 |
3 rows × 190 columns
Input: a taxon name and function nameoutput: A matrix of all peptides intensity under the taxa-funcsw.get_intensity_matrix(taxon_name=taxon, func_name=function)
| V1_01 | V1_02 | V1_03 | V1_04 | V1_05 | V1_06 | V1_07 | V1_08 | V1_09 | V1_10 | ... | V5_29 | V5_30 | V5_31 | V5_32 | V5_33 | V5_34 | V5_35 | V5_36 | V5_37 | V5_38 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sequence | |||||||||||||||||||||
| ALNNADTITVGEC(Carbamidomethyl)SGVTLEEAKK | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 1315398 | 0 | 0 | 0 | 0 | 0 | 0 |
| ALPMHDYEPDREDGLC(Carbamidomethyl)SIR | 0 | 618606 | 0 | 0 | 385705 | 0 | 0 | 138603 | 0 | 137204 | ... | 0 | 0 | 0 | 1422385 | 376129 | 0 | 152559 | 108580 | 0 | 0 |
| DQINREDSVFK | 260958 | 354036 | 0 | 0 | 825274 | 362460 | 0 | 130755 | 0 | 158060 | ... | 502495 | 0 | 158184 | 6929513 | 0 | 230961 | 258840 | 168180 | 0 | 0 |
| EGELPTNWR | 372353 | 2665658 | 759794 | 520188 | 2560633 | 680107 | 0 | 867148 | 336808 | 567680 | ... | 627490 | 0 | 388002 | 5300408 | 922208 | 521595 | 244269 | 305343 | 0 | 503723 |
| IMMDLVVNHTSDEHK | 0 | 412916 | 1035354 | 613620 | 943625 | 0 | 383944 | 762730 | 538389 | 496835 | ... | 639038 | 0 | 881517 | 2511732 | 319958 | 352913 | 364939 | 138788 | 0 | 1202804 |
| INAKDQINREDSVFK | 505599 | 714323 | 830983 | 782399 | 722507 | 868311 | 763122 | 426687 | 716517 | 580215 | ... | 0 | 0 | 0 | 2478282 | 0 | 0 | 0 | 0 | 0 | 0 |
| KSTDNPYR | 309908 | 602749 | 0 | 296602 | 514596 | 289842 | 231717 | 164608 | 0 | 259714 | ... | 0 | 0 | 0 | 809794 | 0 | 0 | 0 | 0 | 0 | 137398 |
| MQWTDGENAGFTTGKPWLK | 376350 | 1181448 | 0 | 0 | 944313 | 0 | 0 | 0 | 0 | 0 | ... | 355923 | 0 | 0 | 1704527 | 258665 | 0 | 0 | 0 | 0 | 0 |
| MTEEDMMAAIGYK | 0 | 435420 | 0 | 0 | 626554 | 0 | 0 | 0 | 0 | 0 | ... | 526201 | 0 | 285410 | 7823039 | 440872 | 339267 | 0 | 289379 | 0 | 0 |
| SFC(Carbamidomethyl)DSN(Deamidated)GDGIGDLN(Deamidated)GITGK | 0 | 248153 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 1117332 | 0 | 0 | 0 | 0 | 0 | 0 |
| SFC(Carbamidomethyl)DSN(Deamidated)GDGIGDLNGITGK | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 2134871 | 0 | 0 | 0 | 0 | 0 | 0 |
| SFC(Carbamidomethyl)DSNGDGIGDLN(Deamidated)GITGK | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 2355751 | 0 | 0 | 0 | 0 | 0 | 0 |
| SFC(Carbamidomethyl)DSNGDGIGDLNGITGK | 0 | 648961 | 0 | 0 | 484536 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 3987066 | 0 | 0 | 0 | 0 | 0 | 511658 |
| TLLVVGNYQKEPQTIELAGEC(Carbamidomethyl)R | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| TPMQWTDGENAGFTTGKPWLK | 378120 | 558761 | 0 | 287484 | 474311 | 0 | 429778 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 995511 | 430143 | 0 | 130989 | 0 | 0 | 0 |
| VLISNYI(Xle->Ser)DAK | 688196 | 4111870 | 391997 | 0 | 3039805 | 874560 | 0 | 872370 | 442626 | 579671 | ... | 493869 | 423337 | 594338 | 9593719 | 665149 | 597041 | 690946 | 559485 | 398924 | 540997 |
| VLISNYIDAK | 0 | 0 | 461146 | 0 | 646190 | 0 | 0 | 492259 | 0 | 0 | ... | 1412480 | 873030 | 821886 | 13582660 | 987505 | 916913 | 995771 | 688161 | 680664 | 778464 |
| VNANYTK | 679608 | 2761562 | 776906 | 590181 | 2082780 | 883184 | 330056 | 1174949 | 1248221 | 1006391 | ... | 860312 | 181193 | 2063425 | 3347602 | 2412606 | 1013492 | 0 | 748867 | 1346680 | 0 |
18 rows × 190 columns
sw.get_intensity_matrix(taxon_name=taxon, func_name=function, groups=['MAL', 'PBS'])
| V1_32 | V2_32 | V3_32 | V4_32 | V5_32 | V1_01 | V1_26 | V1_37 | V2_01 | V2_26 | V2_37 | V3_01 | V3_26 | V3_37 | V4_01 | V4_26 | V4_37 | V5_01 | V5_26 | V5_37 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sequence | ||||||||||||||||||||
| ALNNADTITVGEC(Carbamidomethyl)SGVTLEEAKK | 434741 | 417616 | 1387643 | 695346 | 1315398 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| ALPMHDYEPDREDGLC(Carbamidomethyl)SIR | 337218 | 609524 | 832618 | 612271 | 1422385 | 0 | 203204 | 0 | 0 | 129616 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| DQINREDSVFK | 981283 | 0 | 2455104 | 1620138 | 6929513 | 260958 | 144356 | 0 | 0 | 0 | 443562 | 0 | 0 | 0 | 0 | 0 | 0 | 185677 | 227617 | 0 |
| EGELPTNWR | 3160785 | 1456018 | 4665067 | 3019300 | 5300408 | 372353 | 728259 | 0 | 0 | 0 | 0 | 662900 | 0 | 462996 | 636790 | 0 | 469682 | 0 | 319528 | 0 |
| IMMDLVVNHTSDEHK | 1278639 | 1278804 | 1871439 | 1295025 | 2511732 | 0 | 883181 | 891795 | 644631 | 0 | 651423 | 325094 | 697803 | 1021961 | 571719 | 778144 | 988552 | 0 | 0 | 0 |
| INAKDQINREDSVFK | 945226 | 480514 | 667388 | 735779 | 2478282 | 505599 | 544242 | 962968 | 371219 | 479039 | 576014 | 1042643 | 428329 | 1027263 | 0 | 0 | 0 | 0 | 0 | 0 |
| KSTDNPYR | 616553 | 1196118 | 744606 | 346441 | 809794 | 309908 | 179245 | 264785 | 0 | 0 | 0 | 0 | 118177 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| MQWTDGENAGFTTGKPWLK | 863779 | 601707 | 1544428 | 1251519 | 1704527 | 376350 | 291765 | 0 | 272426 | 0 | 0 | 436508 | 273029 | 448206 | 0 | 444139 | 438718 | 0 | 326660 | 0 |
| MTEEDMMAAIGYK | 636212 | 3450194 | 2791486 | 2246693 | 7823039 | 0 | 0 | 0 | 494686 | 526644 | 371563 | 407551 | 389946 | 611135 | 320991 | 0 | 390194 | 490641 | 0 | 0 |
| SFC(Carbamidomethyl)DSN(Deamidated)GDGIGDLN(Deamidated)GITGK | 475946 | 1018241 | 677051 | 0 | 1117332 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| SFC(Carbamidomethyl)DSN(Deamidated)GDGIGDLNGITGK | 832444 | 1000680 | 1273125 | 931489 | 2134871 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| SFC(Carbamidomethyl)DSNGDGIGDLN(Deamidated)GITGK | 666817 | 1009803 | 1126245 | 1114940 | 2355751 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| SFC(Carbamidomethyl)DSNGDGIGDLNGITGK | 492400 | 1021262 | 1058611 | 2188407 | 3987066 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| TLLVVGNYQKEPQTIELAGEC(Carbamidomethyl)R | 0 | 667588 | 894714 | 681946 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| TPMQWTDGENAGFTTGKPWLK | 0 | 518267 | 1062874 | 374322 | 995511 | 378120 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 339144 | 0 | 0 | 0 | 0 | 0 |
| VLISNYI(Xle->Ser)DAK | 4384464 | 9780422 | 17734368 | 4625617 | 9593719 | 688196 | 398316 | 452609 | 648577 | 727875 | 0 | 1364226 | 1217237 | 959671 | 958381 | 782352 | 905763 | 569983 | 352194 | 398924 |
| VLISNYIDAK | 1859258 | 848574 | 307211 | 4400783 | 13582660 | 0 | 401518 | 0 | 911352 | 613049 | 743575 | 481944 | 810339 | 571172 | 527753 | 356389 | 380404 | 581342 | 736870 | 680664 |
| VNANYTK | 2350871 | 2596435 | 4554566 | 2852711 | 3347602 | 679608 | 647583 | 805761 | 631602 | 764432 | 764567 | 883115 | 1286705 | 1838394 | 769235 | 313378 | 953150 | 291456 | 314828 | 1346680 |
sw.get_top_intensity_matrix_of_test_res(df_ttest, df_type='ttest', top_num=10)
| V1_32 | V2_32 | V3_32 | V4_32 | V5_32 | V1_01 | V1_26 | V1_37 | V2_01 | V2_26 | V2_37 | V3_01 | V3_26 | V3_37 | V4_01 | V4_26 | V4_37 | V5_01 | V5_26 | V5_37 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Taxa-Func | ||||||||||||||||||||
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Belongs to the bacterial ribosomal protein bS16 family] | 3405147 | 2031408 | 3890510 | 3174528 | 3735839 | 495699 | 618303 | 0 | 547513 | 660347 | 0 | 0 | 606541 | 0 | 377076 | 0 | 0 | 0 | 408600 | 0 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A massiliensis [Belongs to the phosphoglycerate kinase family] | 10544927 | 7925416 | 12979505 | 8669368 | 10268308 | 2376259 | 2298544 | 2032377 | 3984972 | 3559154 | 3021435 | 2468879 | 2453278 | 1687110 | 3090003 | 1835245 | 3525475 | 2499385 | 1936377 | 1649894 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Putative cell wall binding repeat] | 4024996 | 2184018 | 2897185 | 3198223 | 3172044 | 467096 | 0 | 290105 | 1289805 | 271961 | 364883 | 606735 | 0 | 618545 | 244241 | 441393 | 63637 | 481833 | 142226 | 870203 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Bacterial extracellular solute-binding protein] | 55357633 | 38368403 | 69739326 | 37982563 | 64018487 | 10357237 | 5822630 | 9279453 | 9944561 | 10069509 | 9029598 | 10329806 | 12966514 | 9913544 | 5018059 | 3957163 | 2260259 | 7135096 | 5804131 | 9991801 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Psort location Cytoplasmic, score 9.98] | 33008066 | 62835342 | 53925379 | 41611821 | 70276260 | 16946312 | 16233511 | 10743316 | 14235220 | 11635923 | 13545490 | 15380275 | 11562475 | 13704287 | 16578006 | 8585544 | 11287176 | 15287787 | 16077613 | 12603490 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Psort location CytoplasmicMembrane, score 9.75] | 673700 | 922783 | 865928 | 576781 | 1037950 | 467309 | 194477 | 78400 | 0 | 0 | 122718 | 243406 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A sp003477525 [Alpha amylase catalytic] | 3287917 | 2910844 | 5938048 | 2417397 | 3601729 | 619484 | 255115 | 374653 | 666260 | 497054 | 748190 | 262388 | 333507 | 271965 | 152341 | 165736 | 0 | 0 | 0 | 0 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Catalyzes the conversion of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR)] | 2012315 | 2331128 | 4225992 | 4520725 | 5936002 | 383915 | 0 | 0 | 0 | 0 | 0 | 417303 | 373176 | 0 | 0 | 0 | 156443 | 0 | 0 | 0 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP] | 6624441 | 5728486 | 13980073 | 7957624 | 12377792 | 818545 | 1213816 | 792025 | 1109360 | 839295 | 961701 | 1488777 | 1909321 | 1141391 | 1507205 | 314757 | 738168 | 1112445 | 0 | 0 |
| d__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A [Converts alpha-aldose to the beta-anomer] | 2979891 | 2552639 | 5769546 | 2785415 | 6061225 | 573312 | 81611 | 410258 | 319646 | 203478 | 144851 | 88940 | 122465 | 0 | 54850 | 0 | 0 | 312584 | 215240 | 108597 |
hp.plot_basic_heatmap(mat=sw.get_intensity_matrix(func_name=function), title='Alpha amylase catalytic')
Table size: 3 x 190 Recommended figure size: width: 40, length: 12, front_title: 20, font_size: 10
<seaborn.matrix.ClusterGrid at 0x187a1f0c5b0>
<Figure size 4000x1200 with 0 Axes>
hp.plot_basic_heatmap(mat=sw.get_intensity_matrix(taxon_name=taxon,func_name=function ), title='Intensity of Blautia_A wexlerae_A - Alpha amylase catalytic')
Table size: 18 x 190 Recommended figure size: width: 40, length: 14.0, front_title: 20, font_size: 10
<seaborn.matrix.ClusterGrid at 0x1879c039880>
<Figure size 4000x1400 with 0 Axes>
some groups we carehp.plot_basic_heatmap(mat=sw.get_intensity_matrix(func_name=function, groups=['MAL', 'PBS'] ), title='Alpha amylase catalytic')
Table size: 3 x 20 Recommended figure size: width: 25, length: 12, front_title: 15, font_size: 10
<seaborn.matrix.ClusterGrid at 0x1879fb66070>
<Figure size 2500x1200 with 0 Axes>
some groupshp.plot_basic_heatmap(mat=sw.get_intensity_matrix(taxon_name=taxon,func_name=function, groups=['MAL', 'PBS'] ), title='Intensity of Blautia_A wexlerae_A - Alpha amylase catalytic')
Table size: 18 x 20 Recommended figure size: width: 25, length: 14.0, front_title: 15, font_size: 10
<seaborn.matrix.ClusterGrid at 0x1879fcc79a0>
<Figure size 2500x1400 with 0 Axes>
lp = LinePlot(sw)
lp.plot_intensity_line(func_name=function, fig_size=(25, 10))
<Axes: title={'center': 'Alpha amylase catalytic'}, xlabel='Samples', ylabel='Intensity'>
lp.plot_intensity_line(taxon_name=taxon,func_name=function, fig_size=(25,10))
<Axes: title={'center': 'd__Bacteria|p__Firmicutes_A|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia_A|s__Blautia_A wexlerae_A\nAlpha amylase catalytic'}, xlabel='Samples', ylabel='Intensity'>